|
Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 16, Number 4, 2009
Contents
Regular Papers
Molecular Dynamics Study of the Internal Water
Molecules in Vasopressin and Oxytocin Receptors Pp.
342-350
M.J. Slusarz, R. Slusarz and J. Ciarkowski
[Abstract] [Purchase
Article] [PMID:
19356129 PubMed - indexed for MEDLINE]
Prediction of Cell Wall Lytic Enzymes
Using Chou’s Amphiphilic Pseudo Amino Acid Composition
Pp. 351-355
H. Ding, L. Luo and H. Lin
[Abstract] [Purchase
Article] [PMID:
19356130 PubMed - indexed for MEDLINE]
Optimized Expression of a Thermostable
Xylanase 11 A gene from Chaetomium thermophilum
NIBGE 1 in Escherichia coli Pp. 356-362
A. Ghaffar, S.A. Khan, Z. Mukhtar, F. Latif
and M.I. Rajoka
[Abstract] [Purchase
Article] [PMID:
19356131 PubMed - indexed for MEDLINE]
EQCM Biosensors Based on DNA Aptamers
and Antibodies for Rapid Detection of Prions Pp.
363-367
T. Hianik, A. Porfireva, I. Grman and
G. Evtugyn
[Abstract] [Purchase
Article] [PMID:
19356132 PubMed - indexed for MEDLINE]
Efficient Gene Transfer to Rat Fetal
Osteoblastic Cells by Synthetic Peptide Vector System
Pp. 368-372
N. Man, L. Yu, F. Zheng, Y. Li and
L.-p. Wen
[Abstract] [Purchase
Article] [PMID:
19356133 PubMed - indexed for MEDLINE]
BSFINDER: Finding Binding Sites of HCV
Proteins Using a Support Vector Machine Pp. 373-382
Y. Chen and K. Han
[Abstract] [Purchase
Article] [PMID:
19356134 PubMed - indexed for MEDLINE]
Structure Prediction of Neuroendocrine
Convertase -2: A Potential Target in Various Cancers Pp.
383-391
A. Polamarasetty, M. Chatterjee, L. Guruprasad
and P. Reddanna
[Abstract] [Purchase
Article] [PMID:
19356135 PubMed - indexed for MEDLINE]
Design and Synthesis of Substrates for
Model Ribosomal Reactions Pp. 392-401
S.G. Bayryamov, N.G. Vassilev, M.A. Rangelov,
A.P. Mladjova and D.D. Petkov
[Abstract] [Purchase
Article] [PMID:
19356136 PubMed - indexed for MEDLINE]
The TPR2B Domain of the Hsp70/Hsp90 Organizing
Protein (Hop) May Contribute Towards Its Dimerization Pp.
402-407
V.M. Longshaw, L.L. Stephens, S. Daniel and G.L. Blatch
[Abstract] [Purchase
Article] [PMID:
19356137 PubMed - indexed for MEDLINE]
Low-Molecular-Weight Aldehyde Inhibitors of
Cathepsin G Pp. 408-410
A. Lesner, M. Wysocka, M. Solek, A. Legowska and
K. Rolka
[Abstract] [Purchase
Article] [PMID:
19356138 PubMed - indexed for MEDLINE]
Roles of the Valine Clusters in Domain
3 of the Hemolytic Lectin CEL-III in Its Oligomerization and
Hemolytic Abilities Pp. 411-414
K. Hisamatsu, H. Unno, S. Goda and T. Hatakeyama
[Abstract] [Purchase
Article] [PMID:
19356139 PubMed - indexed for MEDLINE]
Interaction Between Two Residues in the
Inter-Domain Interface of Escherichia coli Peptidase
N Modulates Catalytic Activity Pp. 415-422
A. Kumar, S. Reddy, N. Srinivasan and
D. Nandi
[Abstract] [Supplementary
Material]
[Purchase
Article] [PMID:
19356140 PubMed - indexed for MEDLINE]
Stability Check of Succinylated Concanavalin
A: Presence of Functionally Active Conformational State
Pp. 423-429
S. Fatima and R.H. Khan
[Abstract] [Purchase
Article] [PMID:
19356141 PubMed - indexed for MEDLINE]
A Plant-Defensin from Sugarcane (Saccharum
spp.) Pp. 430-436
L. Padovan, L. Segat, A. Tossi, N. Antcheva,
A.M. Benko-Iseppon, A.K. Ederson, L. Brandao, T. Calsa Jr.
and S. Crovella
[Abstract] [Purchase
Article] [PMID:
19356142 PubMed - indexed for MEDLINE]
Gastrulation Defective Protease Interacts
with Anionic Components of the Drosophila Ovary Extracellular
Matrix Pp. 437-443
S. Sukumari-Ramesh and E.K. LeMosy
[Abstract] [Purchase
Article] [PMID:
19356143 PubMed - indexed for MEDLINE]
Crystallization Reports
Crystallization of the Altitude Adapted Hemoglobin
of Guinea Pig Pp. 444-446
E. Jaenicke and B. Pairet
[Abstract] [Purchase
Article] [PMID:
19356144 PubMed - indexed for MEDLINE]
Crystallization and Preliminary X-Ray
Analysis of the Low-Affinity Complex Between Human Leukocyte
Antigen-G (HLA-G) and Leukocyte Ig-Like Receptor
B2 (LILRB2) Pp. 447-449
M. Shiroishi and K. Maenaka
[Abstract] [Purchase
Article] [PMID:
19356145 PubMed - indexed for MEDLINE]
Crystallization and Preliminary X-Ray
Diffraction Analysis of ARO9, an Aromatic Aminotransferase
from Saccharomyces cerevisiae Pp. 450-453
H. Chen, H. Huang, X. Li, S. Tong, L. Niu and
M. Teng
[Abstract] [Purchase
Article] [PMID:
19356146 PubMed - indexed for MEDLINE]
Purification, Crystallization and Preliminary
X-Ray Diffraction Studies on Goat (Capra hircus)
Hemoglobin - A Low Oxygen Affinity Species Pp. 454-456
P.S. Moorthy, K. Neelagandan , M. Balasubramanian and
M.N.G. Ponnuswamy
[Abstract] [Purchase
Article] [PMID:
19356147 PubMed - indexed for MEDLINE]
Abstracts
[Back to top]
[Purchase
Article] [PMID:
19356129 PubMed - indexed for MEDLINE]
Molecular Dynamics Study of the Internal Water Molecules
in Vasopressin and Oxytocin Receptors
M.J. Slusarz, R. Slusarz and J. Ciarkowski
The role of the internal water molecules in vasopressin
and oxytocin receptors has been investigated via molecular
dynamics simulations in hydrated membrane model. Several water
molecules have been identified within the binding pockets
of receptors, where they interact with the conserved residues.
In all unliganded receptors, the water molecules bound to
the highly conserved D2.50 cluster have been observed. It
has been proposed which water molecules may significantly
contribute to the stability of overall receptor structure.
In receptor-ligand complexes the water molecules are involved
in the receptor–ligand interactions by forming water-mediated
hydrogen bonds at their contact surface.
[Back to top]
[Purchase
Article] [PMID:
19356130 PubMed - indexed for MEDLINE]
Prediction of Cell Wall Lytic Enzymes Using Chou’s
Amphiphilic Pseudo Amino Acid Composition
H. Ding, L. Luo and H. Lin
Discriminating cell wall lytic enzymes from non lytic
enzymes is a very important task for curing bacterial
infections. In this paper, based on Chou’s amphiphilic
pseudo amino acid composition, we develop fisher-discriminant
based classifier to predict cell wall lytic enzymes.
Experiments show that 66.7% sensitivity with 88.6% specificity
is obtained. The method is further able to predict endolysin
and autolysin with an overall accuracy of 92.9%. Results demonstrated
that our method can provide highly useful information for
further bacterial control research.
[Back to top]
[Purchase
Article] [PMID:
19356131 PubMed - indexed for MEDLINE]
Optimized Expression of a Thermostable Xylanase
11 A gene from Chaetomium thermophilum NIBGE
1 in Escherichia coli
A. Ghaffar, S.A. Khan, Z. Mukhtar, F. Latif
and M.I. Rajoka
The xylanase (Xyn11A) gene (883 bp) was amplified
using C. thermophilum DNA as template and cloned
into pET-32a (+) and expressed in E. coli BL21 under
T7 promoter. The recombinant
xylanase on SDS-PAGE had a molecular mass of 30 kDa. Productivity
profiles of xylanase in E. coli recombinant are more
than 4-fold of that produced from T. reesei RUTC-30,
5-fold of that produced by the donor and significantly higher
than the values reported on other E. coli, and Saccharomyces
cerevisiae recombinants. Temperature stability, pH stability,
and other kinetic parameters confirmed that the gene product
was thermo-stable in alkaline buffer favoring its suitability
to bio-bleaching of kraft pulp.
[Back to top]
[Purchase
Article] [PMID:
19356132 PubMed - indexed for MEDLINE]
EQCM Biosensors Based on DNA Aptamers and Antibodies
for Rapid Detection of Prions
T. Hianik, A. Porfireva, I. Grman and
G. Evtugyn
Novel affinity biosensors for detecting cellular prions,
PrPC, based on DNA aptamers
and antibodies immobilized onto the carbon nanotubes have
been designed and compared in accordance with their binding
ability and analytical performance. The biosensors allowed
us to detect PrPC with the
limits of detection of 20 to 50 pM.
[Back to top]
[Purchase
Article] [PMID:
19356133 PubMed - indexed for MEDLINE]
Efficient Gene Transfer to Rat Fetal Osteoblastic
Cells by Synthetic Peptide Vector System
N. Man, L. Yu, F. Zheng, Y. Li and
L.-p. Wen
We synthesized a 15-amino acid bi-functional synthetic
peptide, RPC2, with the sequence Ac-CGKRKWSQ PKKKRKV-Cysteamide,
which consists of a 7-amino acid nuclear localization signal
(NLS) domain at the carboxyl terminus that electrostatically
binds DNA and a 5-amino-acid tumor-homing domain at the amino
terminus. This peptide efficiently delivered GFP and Renilla
luciferase reporter genes into rat primary osteoblastic cells
while exhibiting low cytotoxicity. The optimal delivery was
achieved when the ratio of DNA: RPC2 reached 1:10 (w/w). Transfection
efficiency can be further enhanced by the addition of Lipofectamine
2000 and modification of RPC2. These results indicated that
RPC2 can deliver exogenous DNA into primary osteoblastic cells
with low cytotoxicity and be potentially utilized in experimental
and clinical applications in the field of bone tissue engineering.
[Back to top]
[Purchase
Article] [PMID:
19356134 PubMed - indexed for MEDLINE]
BSFINDER: Finding Binding Sites of HCV Proteins Using
a Support Vector Machine
Y. Chen and K. Han
Hepatitis C virus (HCV) infection is a major cause of
liver disease and a dangerous threat to public health. Hence,
the problem of finding interactions between HCV and human
proteins has received much attention. In this paper, we present
an approach to predicting binding residues in HCV proteins
using a support vector machine (SVM) classifier. Based on
six biochemical properties of amino acids (sequence profile,
accessible surface area, residue binding propensity, sequence
entropy, hydrophobicity and conservation weight), the SVM
classifier achieved an average accuracy of 93%. Contiguous
residues in the sequence act together to determine a binding
site, and a window of 11 residues (the target residue and
5 adjacent residues on each side) gave the best result in
our study. Our approach has been implemented in a program
called BSFinder (Binding Site Finder), which is available
at http://wilab.inha.ac.kr/bsfinder. BSFinder will be of considerable
help in predicting binding residues and potential interacting
partners of a protein.
[Back to top]
[Purchase
Article] [PMID:
19356135 PubMed - indexed for MEDLINE]
Structure Prediction of Neuroendocrine Convertase
-2: A Potential Target in Various Cancers
A. Polamarasetty, M. Chatterjee, L. Guruprasad
and P. Reddanna
Prohormone or proprotein convertases (PC2) are members
of the subtilisin family of serine proteases. They are involved
in the activation of precursor molecules by endoproteolytic
cleavage at basic amino acid residues within the general motif
(K/R)-(X)n- (K/R)2, where n is 0, 2, 4 or 6 and X
is usually not Cys. Among the members of this prohormone convertase
family, Neuroendocrine Convertase-2 (NEC-2) is regarded as
one of the important proteins involved in the maturation of
many precursor proteins. Being widely distributed in the neuroendocrine
cells, these proteins play a vital role in causing malignant
gliomas. They can serve as important drug targets in the treatment
of cancers. In the present study, a 3D model of NEC-2 was
generated using homology modeling. The model was optimized
by a brief energy minimization in CHARMM and dynamics simulation
of 250ps in MOE. The validation results of PROCHECK and Profile
3D show that the stereochemical quality of the model is good.
The Cα
backbone of the template and the target (NEC-2) when superimposed
showed RMSD of 0.39Å.
The model showed Asp51, His92 and Ser268 in the active site
as seen in most of the PC2 members. The NEC-2 structure differs
from that of furin at the catalytic pocket region with relevance
to the amino acid composition which can be exploited for the
design of specific inhibitors towards NEC-2.
[Back to top]
[Purchase
Article] [PMID:
19356136 PubMed - indexed for MEDLINE]
Design and Synthesis of Substrates for Model Ribosomal
Reactions
S.G. Bayryamov, N.G. Vassilev, M.A. Rangelov,
A.P. Mladjova and
D.D. Petkov
2’/3’-O-[Bz(NO2)-Orn(Boc)]-5’-O-Piv-Ado
(1) and its deoxy analog: 3’-O-[Bz(NO2)-Orn(Boc)]-5’-O-Piv-2’-dAdo
(2) were designed and synthesized as substrates
for the model ribosome reaction we used to demonstrate the
crucial role of A76 2’-OH of peptidyl-tRNA in the rate
acceleration of peptide bond formation during protein biosynthesis.
[Back to top]
[Purchase
Article] [PMID:
19356137 PubMed - indexed for MEDLINE]
The TPR2B Domain of the Hsp70/Hsp90 Organizing Protein
(Hop) May Contribute Towards Its Dimerization
V.M. Longshaw, L.L. Stephens, S. Daniel and G.L.
Blatch
The role of the TPR2B domain of Hop is as yet unknown.
We have shown here by site directed mutagenesis and size exclusion
chromatography for the first time that the TPR1 and TPR2B
domains of Hop independently dimerized, and that the dimerization
of TPR2B was not dependent on its predicted two-carboxylate
clamp residues. Furthermore, our data indicated that the dimerization
of Hop and its domains was not disrupted in the presence of
Hsp70 and Hsp90 peptides.
[Back to top]
[Purchase
Article] [PMID:
19356138 PubMed - indexed for MEDLINE]
Low-Molecular-Weight Aldehyde Inhibitors of
Cathepsin G
A. Lesner, M. Wysocka, M. Solek, A.
Legowska and K. Rolka
A series of aldehyde inhibitors with the general formula
Ac-Phe-Val-Thr-X-CHO, where X = Lys, Arg, Phe, Tyr, p-nitro-L-phenylalanine
(Nif), p-amino-L-phenylalanine
(Amf), p-guanidine-L-phenylalanine
(Gnf), pyridyl-L-alanine (Pal), was
synthesized. The starting structure of this series based on
our previous work on cathepsin G chromogenic substrates. The
synthesis of all compounds was performed in solid phase applying
Fmoc chemistry. We investigated the inhibitory potency of
the obtained compounds against cathepsin G and bovine α-chymotrypsin
and evaluated their dissociation constants (Ki).
The studied peptides displayed different inhibition profiles
and potency. As a result, a potent and selective inhibitor
of cathepsin G with the sequence Ac-Phe-Val-Thr-Gnf-CHO, displaying
Ki = 22 nM was obtained.
[Back to top]
[Purchase
Article] [PMID:
19356139 PubMed - indexed for MEDLINE]
Roles of the Valine Clusters in Domain 3 of the Hemolytic
Lectin CEL-III in Its Oligomerization and Hemolytic Abilities
K. Hisamatsu, H. Unno, S. Goda and T.
Hatakeyama
The hemolytic lectin CEL-III and its site-directed mutants
were expressed in Escherichia coli cells. Replacement
of the valine clusters in domain 3 with alanine residues led
to increased self-oligomerization in solution and higher hemolytic
activity. The results suggest the involvement of these valine
clusters in CEL-III oligomerization and hemolytic activity.
[Back to top]
[Purchase
Article] [PMID:
19356140 PubMed - indexed for MEDLINE]
Interaction Between Two Residues in the Inter-Domain
Interface of Escherichia coli Peptidase N Modulates Catalytic
Activity
A. Kumar, S. Reddy, N. Srinivasan and
D. Nandi
[Supplementary
Material]
The role of interaction between Asn259 (catalytic domain)
with Gln821 (C-terminal domain) in PeptidaseN was investi-gated.
The kcat of PeptidaseN
containing Asn259Asp or Gln821Glu is enhanced whereas it is
suppressed in Asn259AspGln821Glu. Structural analysis shows
this interaction to change the relative disposition of active
site residues, which modulates catalytic activity.
[Back to top]
[Purchase
Article] [PMID:
19356141 PubMed - indexed for MEDLINE]
Stability Check of Succinylated Concanavalin A: Presence
of Functionally Active Conformational State
S. Fatima and R.H. Khan
The equilibrium denaturation pathway of Succinyl Con
A exhibited three-state mechanism with the transition midpoints
at 1 and 3 M GdnHCl and at 2.6 and 5 M urea. Unfolding resulted
in stabilization of molten-globule (MG) like intermediate
states at 2 M GdnHCl and 3 M urea. It was particularly interesting
that state obtained at 3 M urea was functionally active.
[Back to top]
[Purchase
Article] [PMID:
19356142 PubMed - indexed for MEDLINE]
A Plant-Defensin from Sugarcane (Saccharum
spp.)
L. Padovan, L. Segat, A. Tossi, N. Antcheva,
A.M. Benko-Iseppon, A.K. Ederson, L. Brandao, T. Calsa Jr.
and S. Crovella
Comparing available Poaceae defensins with sugarcane
ESTs, a putative defensin gene was identified in sugarcane
and cloned from genomic sugarcane DNA.
The deduced encoded peptide shows the structure and amino
acid composition typical of other plant defensins. Using RT-PCR,
defensin expression in sugarcane and differences between “normal”
and infected sugarcane were evidenced.
[Back to top]
[Purchase
Article] [PMID:
19356143 PubMed - indexed for MEDLINE]
Gastrulation Defective Protease Interacts with Anionic
Components of the Drosophila Ovary Extracellular Matrix
S. Sukumari-Ramesh and E.K. LeMosy
The Drosophila proteases Gastrulation Defective
and Snake function in embryonic polarity establishment and
bind heparin, a surrogate for anionic species present in the
extracellular matrix. Here we demonstrate binding of GD, but
not Snake, to anionic species that appear to be tightly associated
with a highly purified eggshell matrix.
[Back to top]
[Purchase
Article] [PMID:
19356144 PubMed - indexed for MEDLINE]
Crystallization of the Altitude Adapted Hemoglobin
of Guinea Pig
E. Jaenicke and B. Pairet
Hemoglobin is the versatile oxygen carrier in the blood
of vertebrates and a key factor for adaptation to live in
high altitudes. Several structural changes are known to account
for increased oxygen affinity in hemoglobin of altitude adapted
animals such as llama and barheaded goose. Guinea pigs are
adapted to live in high altitudes in the Andes and consequently
their hemoglobin has an increased oxygen affinity. However,
the structural changes responsible for the adaptation of guinea
pig hemoglobin are unknown. Here we report the crystallization
of guinea pig hemoglobin in the presence of 2.6 M ammonium
sulfate and a preliminary analysis of the crystals. Crystals
diffract up to a resolution of 2.0 Å.
They are orthorhombic with space group C 2 2 21
and cell dimensions α
= 84.08 Å,
b = 90.21 Å
and c = 83.44 Å.
[Back to top]
[Purchase
Article] [PMID:
19356145 PubMed - indexed for MEDLINE]
Crystallization and Preliminary X-Ray Analysis of
the Low-Affinity Complex Between Human Leukocyte Antigen-G
(HLA-G) and Leukocyte Ig-Like Receptor B2 (LILRB2)
M. Shiroishi and K. Maenaka
Human leukocyte antigen-G (HLA-G) is a nonclassical MHC
class I (MHCI) molecule that is expressed mainly on placenta
trophoblast cells. Leukocyte Ig-like receptor B2 (LILRB2)
is a human inhibitory immune receptor that recognizes HLA-G
with a higher affinity than any other MHCI although this interaction
is only in the μM
range. The interaction between HLA-G and LILRB2 seems to play
a dominant role in the escape of the fetus from the maternal
immune response. Here we report the crystallization and x-ray
analysis of the LILRB2/HLA-G complex. The extracellular domains
of HLA-G and LILRB2 were expressed in Escherichia coli,
refolded and purified. The initial crystallization trials
using novel PEG-based screening sets provided crystals of
the LILRB2/HLA-G complex with 40-50% PEG400 as the precipitant.
These crystals belong to space group P3121
(a=b=81.4 Å,
c=186.7 γ,
“=120º).
Dehydration of the crystals by soaking them in a solution
containing a higher concentration of PEG400 dramatically improved
the resolution and also the mosaicity.
[Back to top]
[Purchase
Article] [PMID:
19356146 PubMed - indexed for MEDLINE]
Crystallization and Preliminary X-Ray Diffraction
Analysis of ARO9, an Aromatic Aminotransferase from Saccharomyces
cerevisiae
H. Chen, H. Huang, X. Li, S. Tong, L. Niu and
M. Teng
Saccharomyces cerevisae ARO9 protein, an aromatic aminotransferase
II, catalyzes the transamination step of the catabolism of
aromatic amino acids, mainly tryptophan. ARO9 also belongs
to a novel subfamily of enzymes within the aminotransferase
subgroup I. Crystals of ARO9 protein have been grown using
the hanging-drop vapour-diffusion method. The crystals belong
to the orthorhombic space group P212121,
with unit-cell parameters a = 75.6 Å,
b = 117.5 Å,
c = 134.9 Å.
Diffraction data were collected to a resolution of 2.6 Å
using a rotating-anode X-ray source. Analysis indicates the
presence of two molecules in an asymmetric unit.
[Back to top]
[Purchase
Article] [PMID:
19356147 PubMed - indexed for MEDLINE]
Purification, Crystallization and Preliminary X-Ray
Diffraction Studies on Goat (Capra hircus) Hemoglobin
- A Low Oxygen Affinity Species
P.S. Moorthy, K. Neelagandan , M. Balasubramanian
and M.N.G. Ponnuswamy
Hemoglobin is a vital protein present in almost all higher
species. It is a transport protein involved in carrying oxygen
from lungs to tissues and carbon dioxide back to lungs by
an intrinsically coordinated manner. Even though a good amount
of work has been carried out in this direction there exists
scarcity of structural insight on low oxygen affinity species.
Attempts are being made to unravel the structural insight
of this low oxygen affinity species. Goat blood plasma was
collected, treated with EDTA to avoid blood clotting and purification
was accomplished using DEAE-anion chromatographic column.
The goat hemoglobin was crystallized using 50mM of phosphate
buffer at pH 6.7 with 1M NaCl and PEG 3350 as precipitant
by hanging drop vapor diffusion method. Crystals obtained
are screened and suitable crystals are taken for data collection
using mar345dtb as image plate detector system. Goat
hemoglobin crystal diffracted up to 2.61 Å
resolution. Goat hemoglobin crystallizes in orthorhombic space
group P212121
as a whole biological molecule in the asymmetric unit with
cell dimensions a=53.568Å,
b=67.365Å,
c=154.183Å.
|
